Dirofilaria immitis and D. repens are globally distributed mosquito-borne parasitic filarial nematodes. Data on the prevalence of Dirofilaria spp. is not aggregated or publicly available at the national level for countries in North Africa and the Middle East. A systematic review and meta-analysis of publications describing cases of D. immitis and D. repens in 21 countries in North Africa and the Middle East was performed following PRISMA guidelines to estimate the prevalence of Dirofilaria spp. where national and regional estimates don’t exist. In total, 460 publications were reviewed, and 34 met all inclusion criteria for the meta-analysis model. This analysis found that the combined prevalence of Dirofilaria spp. in the included countries was 2.4% (95% CI: 1.6–3.6%; I2 = 81.7%, 95% CI: 78.6–84.3%). Moderator analysis showed a statistically significant difference in the prevalence estimate between diagnostic test methods used. The model detected a high degree of heterogeneity among studies and publication bias. Removal of model identified outliers reduced the estimated prevalence from 2.4% to 1.0%, whereas the trim-and-fill analysis suggested a higher adjusted prevalence (12%). Despite these findings, Dirofilaria spp. prevalence is likely dynamic due to seasonal variations in mosquito vector populations and differences in local mosquito control practices. Additional studies from the countries in and surrounding this region are needed to better identify key risk factors for Dirofilaria spp. in domestic canids and other species (including humans) to inform prevention and control decisions to limit further transmission.